Hybrid polyketide synthases

ABSTRACT

The present invention provides for a polyketide synthase (PKS) capable of synthesizing an even-chain or odd-chain diacid or lactam or diamine. The present invention also provides for a host cell comprising the PKS and when cultured produces the even-chain diacid, odd-chain diacid, or KAPA. The present invention also provides for a host cell comprising the PKS capable of synthesizing a pimelic acid or KAPA, and when cultured produces biotin.

This application is the U.S. National Stage entry of InternationalApplication No. PCT/US2011/058660, filed Oct. 31, 2011, which claimsbenefit of priority to U.S. provisional application No. 61/408,411,filed Oct. 29, 2010, each of which application is herein incorporated byreference for all purposes.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH OR DEVELOPMENT

This invention was made with government support under Contract No.DE-AC02-05CH11231 awarded by the U.S. Department of Energy and Award No.0540879 awarded by the National Science Foundation. The government hascertain rights in the invention

REFERENCE TO A “SEQUENCE LISTING SUBMITTED AS A TEXT FILE

The Sequence Listing written in file SEQTXT_77429-865771-010110US.txt,created on Apr. 22, 2013, 14,668 bytes, machine format IBM-PC,MS-Windows operating system, is hereby incorporated by reference.

FIELD OF THE INVENTION

This invention relates to the production of useful compounds withpolyketide synthases.

BACKGROUND OF THE INVENTION

Dicarboxylic acids (diacids) are important compounds that are used inthe manufacture of commercial polymers (e.g. polyesters, polyurethanes).The use of hybrid polyketide synthases to produce diacids having acarbon backbone with an odd number of carbon atoms is disclosed inInternational Patent Application Publication No. WO 2009/121066.However, commercial polymers are typically produced from reactantsderived from petroleum and petrochemicals.

For example, as illustrated in FIG. 1, the dicarboxylic acid adipic acid[1] is used mainly as a monomer in the production of nylon 6,6 [2], apolyamide generated through the reaction of [1] with hexane-1,6-diamine.Polyesters (for use in fabrics and plastics of many compositions) areformed through the polymerization of terephthalic acid [3] and adialcohol (diol) such as ethylene glycol (to make polyethyleneterephthalate [4]), propane diol (poly(1,3-propanediol terephthalate)[5]) or butanediol (poly(1,4-butanediolphthalate) [6]. Adipic acid isalso used in the synthesis of various polyesters. Currently adipic acidis synthesized via oxidation of cyclohexane and similar petrochemicalsusing traditional chemical synthesis.

Lactams are important compounds useful in the manufacture of a varietyof compounds, including commercial polymers, particularly polyamidessuch as Nylon 6 and Nylon 12. Caprolactam is the sole source of Nylon 6,which is used in the production of durable fibers for carpets and inother products. Larger chain lactams, such as Nylon 12, are used inengineering plastics where their physical properties make them moredesirable. The open chain form of these molecules are also accessibleusing the technology described herein. These cognate acids are also usedin many of the same applications. For example, 6-aminohexanoic acid isthe open chain form of caprolactam and can also be polymerized toproduce Nylon 6.

Diamines are used extensively in the production of polymers,predominantly Nylons, as described above.

The large scale worldwide use of nylons and polyesters requires theproduction of millions of metric tons of adipic acid, caprolactam and1,6-hexanediamine annually. The diacids, lactams, and diamines arethemselves synthesized from starting materials extracted from petroleum.There is a need for new methods to synthesize such compounds in a mannerthat reduces dependence on oil.

Complex polyketides comprise a large class of natural products that aresynthesized in bacteria (mainly members actinomycete family; e.g.Streptomyces), fungi and plants. Polyketides form the aglycone componentof a large number of clinically important drugs, such as antibiotics(e.g. erythromycin, tylosin), antifungal agents (e.g. nystatin),anticancer agents (e.g. epothilone), immunosuppressives (e.g.rapamycin), etc. Though these compounds do not resemble each othereither in their structure or their mode of action, they share a commonbasis for their biosynthesis, which is carried out by a group of enzymesdesignated polyketide synthases. Polyketide synthases (PKS) employ shortchain fatty acyl CoAs in Claisen condensation reactions to producepolyketides. Unlike fatty acid synthases, which utilize acetyl CoA asthe starter and malonyl CoA as the extender units and which use a singlemodule iteratively to produce the nascent acyl chains, PKSs are composedof multiple, discrete modules, each catalyzing the chain growth of asingle step. The present invention provides methods and compositions foremploying polyketide synthases to produce diacids, lactams, diamines,e.g., for the production of commercial polymers.

BRIEF SUMMARY OF THE INVENTION

The present invention provides for a polyketide synthase (PKS), and/oroptionally non-ribosomal peptide synthase and/or CoA ligase, capable ofsynthesizing an even-chain or odd-chain diacid or lactam or diamine. ThePKS is not a naturally occurring PKS. In some embodiments of theinvention, the even-chain or odd-chain diacid or lactam or diamine isnot a compound synthesized by a naturally occurring PKS. In someembodiments of the invention, the PKS is a hybrid PKS comprisingmodules, domains, and/or portions thereof from two or more naturallyoccurring PKSs.

The present invention also provides for a recombinant nucleic acid thatencodes a polyketide synthase (PKS) of the present invention. Therecombinant nucleic acid can be replicon capable of stable maintenancein a host cell. In some embodiments, the replicon is stably integratedinto a chromosome of the host cell. In some embodiments, the replicon isa plasmid. The present invention also provides for a vector orexpression vector comprising a recombinant nucleic acid of the presentinvention. The present invention additionally provides for a host cellcomprising any of the recombinant nucleic acid and/or PKS of the presentinvention. In some embodiments, the host cell, when cultured under asuitable condition, is capable of producing an even- or odd-chaindiacid, lactam, or diamine.

The present invention provides a method of producing an even-chain orodd-chain diacid or lactam or diamine, comprising: providing a host cellof the present invention, and culturing said host cell in a suitableculture medium such that the even-chain or odd-chain diacid or lactam ordiamine is produced.

The present invention provides for a composition comprising aneven-chain or odd-chain diacid or lactam or diamine isolated from a hostcell from which the even-chain or odd-chain diacid or lactam or diaminewas produced, and trace residues and/or contaminants of the host cell.Such trace residues and/or contaminants include cellular materialproduced by the lysis of the host cell. In some embodiments of theinvention, the trace residues and/or contaminants do not or essentiallydo not interfere or retard a polymerization reaction involving theeven-chain or odd-chain diacid or lactam or diamine. The presentinvention also provides these compounds in substantially pure form aswell as methods for using these compounds to make other usefulcompounds, such as commercial polymers.

The present invention provides for a polyketide synthase (PKS) capableof synthesizing malonic acid. The present invention provides for arecombinant nucleic acid that encodes a polyketide synthase (PKS)capable of synthesizing malonic acid. The present invention provides fora host cell comprising any of the recombinant nucleic acid and/or PKS ofthe present invention, wherein when cultured under a suitable conditionthe host cell is capable of producing malonic acid. The presentinvention provides a method of producing malonic acid, comprising:providing a host cell of the present invention, and culturing said hostcell in a suitable culture medium such that the malonic acid isproduced. The present invention provides for a composition comprising amalonic acid isolated from a host cell from which the malonic acid isproduced, and trace residues and/or contaminants of the host cell.

The present invention provides for a polyketide synthase (PKS) capableof synthesizing pimelic acid, 7-keto-8-amino-pelargonic acid (KAPA), orbiotin. The present invention provides for a recombinant nucleic acidthat encodes a polyketide synthase (PKS) capable of synthesizing pimelicacid (KAPA). The present invention provides for a host cell comprisingany of the recombinant nucleic acid and/or PKS of the present invention,wherein when cultured under a suitable condition the host cell iscapable of producing the pimelic acid or KAPA, and optionally biotin.The present invention provides a method of producing pimelic acid orKAPA, and optionally biotin, comprising: providing a host cell of thepresent invention, and culturing said host cell in a suitable culturemedium such that the pimelic acid or KAPA, and optionally biotin, isproduced. The present invention provides for a composition comprising apimelic acid or KAPA, and optionally biotin, isolated from a host cellfrom which the pimelic acid or KAPA, and optionally biotin, is produced,and trace residues and/or contaminants of the host cell.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing aspects and others will be readily appreciated by theskilled artisan from the following description of illustrativeembodiments when read in conjunction with the accompanying drawings.

FIG. 1 shows the various reactions using diacids in the manufacture ofcommercial polymers (e.g. polyesters, polyurethanes). The diacid adipicacid [1] is used as a monomer in the production of nylon [2], apolyamide generated through the reaction of [1] with hexane-1,6-diamine.Polyesters are formed through the polymerization of terephthalic acid[3] and a dialcohol (diol) such as ethylene glycol (to make polyethyleneterephalate [4]), propane diol (poly(1,3-propanediol terephthalate) [5])or butanediol (poly(1,4-butanediolphthalate) [6].

FIG. 2 shows types of modules employed and corresponding precursorsutilized for incorporation into polyketide chains. The loading module isdesignated S. The remaining compounds represent the structuresincorporated into the growing polyketide chain employing extendermodules A-P. The dashed line indicates the C—C bond formed throughClaisen condensation; atoms to the right of the bond and the C atom atthe left of the dashed line represent the structures determined by themodule employed. The R group represents the existing acyl chain prior toincorporation determined by the module.

FIG. 3 shows a scheme for making polyamides or polyesters usingeven-chain diacids.

FIG. 4 shows the native loading and 1^(st) extension of thechondrochlorens PKS as catalyzed by CndA.

FIG. 5 shows the addition of a thioesterase domain resulting in therelease of the free acid product.

FIG. 6 shows a model of the E. coli succinyl-CoA synthetase.

FIG. 7 shows: (A) replacement of the CoA ligase domain with asuccinyl-CoA synthetase and (B) manipulation of the AT specificity ofthe extension domain.

FIG. 8 shows: (A) the native chemistry of the etnangien loading module(Menche et al., J. Am. Chem. Soc. (2008) 130: 14234-14243; herebyincorporated by reference), and (B) the proposed truncation of thisprotein and fusion to a malonate-specific extender module andthioesterase hybrid PKS to yield adipic acid.

FIG. 9 shows the biosynthesis of 7-keto-8-amino-pelargonic acid (KAPA)using a NRPS-PKS hybrid of the present invention.

FIG. 10 shows the pathway from which pimelic acid and/or KAPA isconverted into biotin (or Vitamin H).

FIG. 11 shows the model for the PKS/NRPS hybrid system described inExample 1.

FIG. 12 shows spirofungin A [16-1] is a dicarboxylic acid composed oftwenty-four carbons in its polyketide backbone that is organized into aspiroketal sub-structure. It is produced by the bacterium Streptomycesviolaceusniger Tü 4113. Reveromycin [16-2], produced from Streptomycessp. SN-593 has a similar backbone and spiroketal substructure butdiffers from spirofungin in the atoms shown in blue.

FIG. 13 shows a pathway to convert the final PKS-bound acyl intermediateto spirofungin.

FIG. 14 shows the composition of the PKS and biochemical scheme for theproduction of adipic acid in accordance with an embodiment of theinvention.

FIG. 15 shows the early steps in the biosynthesis of etnangien.

FIG. 16 shows the biosynthesis of adipic acid employing module 1 of theetnangien PKS in accordance with an embodiment of the invention.

FIG. 17 shows the biosynthesis of adipic acid employing module 1 of theetnangien PKS in another embodiment of the invention.

FIG. 18 shows the pathway of glucose to malonic acid employing a threedomain chimeric PKS module in accordance with an embodiment of theinvention.

FIG. 19 shows the pathway of glucose to malonic acid employing adidomain PKS module and a type II thioesterase in accordance with anembodiment of the invention.

FIG. 20 shows the pathway of glucose to malonic acid employing atrans-AT PKS module and the associated AT protein in accordance with anembodiment of the invention. The KS* indicates that this domain iscatalytically inactive, but included for structural reasons.

FIG. 21 shows a scheme for the biosynthesis of caprolactam.

FIG. 22 shows the biosynthetic pathway of the HABA side chain ofbutirosin.

FIG. 23 shows a scheme for the biosynthesis of caprolactam inaccordance, with an embodiment of the invention.

FIG. 24 shows a scheme for the biosynthesis of caprolactam in accordancewith an embodiment of the invention.

FIG. 25A-25C shows schemes for the biosynthesis of 6-aminocaproic acidin accordance with an embodiment of the invention.

FIG. 26A-26C shows a scheme for the biosynthesis of hexane-1,4-diaminein accordance with an embodiment of the invention.

FIG. 27A-27E provides a general schematic for producing odd and evenchain diacids, lactams and cognate acids, and diamines.

DETAILED DESCRIPTION OF THE INVENTION

Before the present invention is described, it is to be understood thatthis invention is not limited to particular embodiments described, assuch may, of course, vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting, since the scope ofthe present invention will be limited only by the appended claims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimits of that range is also specifically disclosed. Each smaller rangebetween any stated value or intervening value in a stated range and anyother stated or intervening value in that stated range is encompassedwithin the invention. The upper and lower limits of these smaller rangesmay independently be included or excluded in the range, and each rangewhere either, neither or both limits are included in the smaller rangesis also encompassed within the invention, subject to any specificallyexcluded limit in the stated range. Where the stated range includes oneor both of the limits, ranges excluding either or both of those includedlimits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any method's andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present invention, the preferred methodsand materials are now described. All publications mentioned herein areincorporated herein by reference to disclose and describe the methodsand/or materials in connection with which the publications are cited.

It must be noted that as used herein and in the appended claims, thesingular forms “a”, “and”, and “the” include plural referents unless thecontext clearly dictates otherwise. Thus, for example, reference to “adiacid” includes a plurality of such diacids, and so forth.

The term “diacid” refers to a hydrocarbon possessing two carboxylic acidmoieties bridged by a chain, or backbone, or one or more carbons. Thebranching and oxidative state of the carbon backbone is variable, asdescribed within.

The term “even-chain diacid” refers to a diacid with a carbon backbone,i.e., disregarding any functional groups or substituents, with an evennumber of carbon atoms.

The term “odd-chain diacid” refers to a diacid with a carbon backbone,i.e., disregarding any functional groups or substituents, with an oddnumber of carbon atoms.

The term “lactam” refers to a heterolcyclic hydrocarbon containing anamide bond in the ring. The technology described herein allows theproduction of either the lactam or the cognate acid form to any lactamdescribed (e.g. 6-aminohexanoic acid is the cognate acid ofcaprolactam). The terms “open chain lactam” or “lactam cognate acid” areused to describe the hydrolyzed form of the lactam, a hydrocarbon chainpossessing a carboxylate at one end and a pendent amino group. The term“lactam” as used herein encompasses both of these chemical classes. Likethe diacids, the branching and oxidative state of the carbons in thebackbone is controlled as described herein. The lactams contain even orodd numbers of carbon atoms in the carbon backbone.

The term “diamine” refers to two amine moieties bridged by a hydrocarbonchain, or backbone, or one or more carbons. As is the case with thediacids and lactams, the branching and oxidative state of the carbonbackbone is variable by design, as described herein. “Diamine” refers toa diamine with a carbon backbone, i.e., disregarding any functionalgroups or substituents, with an odd or even number of carbon atoms.

The term “functional variant” describes an enzyme that has a polypeptidesequence that is at least 70%, 75%, 80%, 85%, 90%, 95% or 99% identicalto any one of the enzymes described herein. The “functional variant”enzyme may retain amino acids residues that are recognized as conservedfor the enzyme, and may have non-conserved amino acid residuessubstituted or found to be of a different amino acid, or amino acid(s)inserted or deleted, but which does not affect or has insignificanteffect its enzymatic activity as compared to the enzyme describedherein. The “functional variant” enzyme has an enzymatic activity thatis identical or essentially identical to the enzymatic activity of theenzyme described herein. The “functional variant” enzyme may be found innature or be an engineered mutant thereof.

These and other objects, advantages, and features of the invention willbecome apparent to those persons skilled in the art upon reading thedetails of the invention as more fully described below.

Polyketide Synthases (PKS)

The present invention provides for a polyketide synthase (PKS) orPKS/non-ribosomal peptide synthetase (NRPS) hybrid capable ofsynthesizing an even-chain or odd-chain diacid, or lactam, or diamine.The PKS or PK/NRPS is not naturally occurring. In some embodiments ofthe invention, the even-chain or odd-chain diacid, or lactam, or diamineis not a compound synthesized by a naturally occurring PKS or PKS/NRPS.In some embodiments of the invention, the PKS is a hybrid PKS comprisingmodules, domains, and/or portions thereof from two or more PKSs. Sucheven-chain or odd-chain diacids, or lactams, or diamines include thediketides and triketides, and polyketides of more than three ketideunits, such as 4, 5, or 6 or more ketide units. The even-chain orodd-chain diacids, or lactams, or diamines can further include one ormore functional groups. Such functional groups include, but are notlimited to, ethyl, methyl and hydroxyl side chains, and internal olefinsand ketones.

PKSs employ short chain fatty acyl CoAs in Claisen condensationreactions to produce polyketides. Unlike fatty acid synthases whichutilize acetyl CoA as the starter and malonyl CoA as the extender units,and use a single module iteratively to produce the nascent acyl chains,PKSs are composed of discrete modules, each catalyzing the chain growthof a single step. Modules can differ from each other in composition sothat overall, a number of different starters (e.g. acetyl CoA, propionylCoA) and extenders, some of which contain stereospecific methyl (orethyl) side chains can be incorporated. In addition, PKS modules do notalways reduce the 3-carbonyl formed from condensation but may leave iteither unreduced (ketone), partially reduced (hydroxyl, 2,3-ene) orfully reduced (3-methylene). Many polyketide synthases employ malonylCoA or [S]-2-methylmalonyl CoA as the starter for polyketide synthesis.In such cases the terminal carboxyl group is usually removed by adecarboxylase domain present at the N-terminus of the correspondingloading domain of the PKS. In summary, the structure (and chirality) ofthe α-carbon and β-carbonyl is determined by the module of the PKSemployed in the synthesis of the growing chain at each particular step.Because of the correspondence between use of modules in the synthesisand the structure of the polyketide produced, it is possible to programthe synthesis to produce a compound of desired structure by selectionand genetic manipulation of polyketide synthases. FIG. 2 shows thevarious modules and the precursor utilized by each module forincorporation into the corresponding nascent acyl (polyketide) chain togive rise to the range of compounds of interest. Table 1 provides a PKSsource for each module. Each PKS source is well-known to one skilled inthe art is readily available. In addition, for each module taught inTable 1, there may be many other modules from other PKS that can beused.

TABLE 1 PKS sources of the various modules. Module PKS Source S1Spirofungin PKS Loading Domain S2 Chondrochloren PKS Loading Domain(with CoA ligase domain replaced with Succinyl CoA Ligase) A RifamycinPKS Module 2 B Oligomycin PKS Module 1 C Spiramycin PKS Module 1 DPikromycin PKS Module 2 E Oligomycin PKS Module 3 F Erythromycin PKSModule 3 G Oligomycin PKS Module 5 H Primaricin PKS Module 7 I TylosinPKS Module 1 J Erythromycin PKS Module 1 K Avermectin PKS Module 7 LRapamycin PKS Module 1 M Erythromycin PKS Module 4 N Pederin Module 2 OAscomycin Module 4 P FK506 Module 4

All extender modules carry the β-acyl ACP synthase (commonly called theketosynthase or KS) domain, which conducts the decarboxylativecondensation step between the extender and the growing polyketide chain,and the acyl carrier protein (ACP) domain that carries the growing acylchain and presents it to the cognate reductive domains for reduction ofthe β-carbonyl. Modules can differ from each other in composition sothat a number of different starter and extender units, some of whichcontain stereospecific side chains (e.g. methyl, ethyl, propylene) canbe incorporated. The acyltransferase (AT) domain of each moduledetermines the extender unit (e.g. malonyl CoA, methylmalonyl CoA, etc.)incorporated. In addition, PKS modules do not always reduce theβ-carbonyl formed from condensation but may leave it either unreduced(ketone), partially reduced (hydroxyl, 2,3-ene) or fully reduced(3-methylene), as shown in FIG. 2. The ketoreductase (KR) domain reducesthe ketone to the OH function (stereospecifically); the dehydratase (DH)domain removes water from the α and β carbons leaving an α,βtrans-double bond; the enoylreductase (ER) domain reduces the doublebond to a β-methylene center; the reductive state of the β-carbonyl,therefore, is determined by the presence of functional reductive domainsin the corresponding module. Less commonly, modules are found to containan additional C-methylation domain (yielding an additional α-methyl sidechain, as in epothilone). The makeup of the PKS, therefore, determinesthe choice of starter and extender acyl units incorporated, the extentof reduction at each condensation step, and the total number of unitsadded to the chain. The wide diversity of structures of polyketides seenin nature is attributed to the diversity in PKS compositions.

A partial list of sources of PKS sequences that can be used in makingthe PKSs of the present invention, for illustration and not limitation,includes Ambruticin (U.S. Pat. No. 7,332,576); Avermectin (U.S. Pat. No.5,252,474; MacNeil et al., 1993, Industrial Microorganisms: Basic andApplied Molecular Genetics, Baltz, Hegeman, & Skatrud, eds. (ASM), pp.245-256; MacNeil et al., 1992, Gene 115: 119-25); Candicidin (FRO008)(Hu et al., 1994, Mol. Microbiol. 14: 163-72); Epothilone (U.S. Pat. No.6,303,342); Erythromycin (WO 93/13663; U.S. Pat. No. 5,824,513; Donadioet al., 1991, Science 252:675-79; Cortes et al., 1990, Nature348:176-8); FK506 (Motamedi et al., 1998, Eur. J. Biochem. 256:528-34;Motamedi et al., 1997, Eur. J. Biochem. 244:74-80); FK520 or ascomycin(U.S. Pat. No. 6,503,737; see also Nielsen et al., 1991, Biochem.30:5789-96); Jerangolid (U.S. Pat. No. 7,285,405); Leptomycin (U.S. Pat.No. 7,288,396); Lovastatin (U.S. Pat. No. 5,744,350); Nemadectin(MacNeil et al., 1993, supra); Niddamycin (Kakavas et al., 1997, J.Bacteriol. 179:7515-22); Oleandomycin (Swan et al., 1994, Mol. Gen.Genet. 242:358-62; U.S. Pat. No. 6,388,099; Olano et al., 1998, Mol.Gen. Genet. 259:299-308); Pederin (PCT publication no. WO 2003/044186);Pikromycin (Xue et al., 2000, Gene 245:203-211); Pimaricin (PCTpublication no. WO 2000/077222); Platenolide (EP Pat. App. 791,656);Rapamycin (Schwecke et al., 1995, Proc. Natl. Acad. Sci. USA92:7839-43); Aparicio et al., 1996, Gene 169:9-16); Rifamycin (August etal., 1998, Chemistry & Biology, 5: 69-79); Soraphen (U.S. Pat. No.5,716,849; Schupp et al., 1995, J. Bacteriology 177: 3673-79);Spiramycin (U.S. Pat. No. 5,098,837); Tylosin (EP 0 791,655; Kuhstoss etal., 1996, Gene 183:231-36; U.S. Pat. No. 5,876,991). Additionalsuitable PKS coding sequences are readily available to one skilled inthe art, or remain to be discovered and characterized, but will beavailable to those of skill (e.g., by reference to GenBank). Each of thereferences cited is hereby specifically and individually incorporated byreference.

Of the more than one hundred PKSs examined, the correspondence betweenuse of modules in the biosynthesis and the structure of the polyketideproduced is fully understood both at the level of the protein sequenceof the PKS and the DNA sequence of the corresponding genes. Theprogramming of modules into polyketide structure can be identified bysequence determination. It is possible to clone or synthesize DNAsequences corresponding to desired modules and transfer them as fullyfunctioning units to heterologous, otherwise non-polyketide producinghosts such as E. coli (B. A. Pfeifer, S. J. Admiraal, H. Gramajo, D. E.Cane, C. Khosla, Science 291, 1790 (2001); hereby incorporated byreference) and Streptomyces (C. M. Kao, L. Katz, C. Khosla, Science 265,509 (1994); hereby incorporated by reference). Additional genes employedfor polyketide biosynthesis have also been identified. Genes thatdetermine phosphopantetheine:protein transferase (PPTase) that transferthe 4-phosphopantetheine co-factor of the ACP domains, commonly presentin polyketide producing hosts, have been cloned in E. coli and otherhosts (K. J. Weissman, H. Hong, M. Oliynyk, A. P. Siskos, P. F. Leadlay,Chembiochem 5, 116 (2004); hereby incorporated by reference). It is alsopossible to re-program polyketide biosynthesis to produce a compound ofdesired structure by either genetic manipulation of a single PKS or byconstruction of a hybrid PKS composed of modules from two or moresources (K. J. Weissman, H. Hong, M. Oliynyk, A. P. Siskos, P. F.Leadlay, Chembiochem 5, 116 (2004); hereby incorporated by reference).

Recombinant methods for manipulating modular PKS genes to make the PKSsof the present invention are described in U.S. Pat. Nos. 5,672,491;5,843,718; 5,830,750; 5,712,146; and 6,303,342; and in PCT publicationnos. WO 98/49315 and WO 97/02358; hereby incorporated by reference. Anumber of genetic engineering strategies have been used with variousPKSs to demonstrate that the structures of polyketides can bemanipulated to produce novel polyketides (see the patent publicationsreferenced supra and Hutchinson, 1998, Curr. Opin. Microbiol. 1:319-329,and Baltz, 1998, Trends Microbiol. 6:76-83; hereby incorporated byreference). In some embodiments, the components of the hybrid PKS arearranged onto polypeptides having interpolypeptide linkers that directthe assembly of the polypeptides into the functional PKS protein, suchthat it is not required that the PKS have the same arrangement ofmodules in the polypeptides as observed in natural PKSs. Suitableinterpolypeptide linkers to join polypeptides and intrapolypeptidelinkers to join modules within a polypeptide are described in PCTpublication no. WO 00/47724, hereby incorporated by reference.

FIG. 27 provides a schematic for the hybrid PKS of the invention usedfor producing the odd chain diacids (A) and even chain diacids (B),lactams (C) and cognate amino acids (D), and diamines (E). By changingthe chemistry incorporated at the start of the process, the terminalfunctionality (acid or amine) and odd vs. even number of carbons in thelinear backbone is established. The number and composition of theintervening modules dictates the total number of carbons as well as thebranching and oxidative state of the carbon chain. The chain releasemechanism of the TE domain, or R+MxcL in the case of E. coli, isresponsible for the final form of the molecule as a free acid, lactam,amino acid or diamine. In FIG. 27A, the system loads malonate andextends with two additional malonate (each from malonyl-CoA) using afull reductive cycle with each extension. In this example, a hydrolyticTE domain is used to release the free carboxylate, in this case pimelicacid. In FIG. 27B, the system incorporates succinate using an NRPSloading module, then extends with malonate and fully reducesintermediate, then releases adipic acid. Thus, by changing the loadingmodule and module depicted in FIG. 27A to the NRPS illustrated in FIG.27B, the chain length and odd vs. even carbon count is also changed. Byswitching the malonate loading module depicted in FIG. 27A to an NRPSloading module specific for glycine, 6-aminohexanoic acid can be made,as illustrated in FIG. 27D. By changing the thioesterase domain depictedin FIG. 27D to one known to catalyze lactonization, the same system canrelease the product as a lactam, as shown in FIG. 27C. If thisthioesterase is changed to an R domain and complemented with an aminotransferase, such as MxcL, the same system can be used to biosynthesizehexane-1,6-diamine (FIG. 27E).

In some embodiments of the invention, the even-chain diacid has thefollowing chemical structure:

wherein each R₁ is independently H, OH, OCH₃, CH₂CH₃, or CH₃, each R₂ isindependently a carbonyl, H or OH, n is an integer, αβ is (1) a singlebond or (2) a double bond, with the proviso that when an αβ is a doublebond then the corresponding R₂ is H and n indicates the number oftwo-carbon-chain subunits in the carbon backbone of the even-chaindiacid. Within each molecule of the even-chain diacid, the R₁, R₂, andαβ within each two-carbon-subunit can be independent of (and so can beidentical to or different from) the R₁, R₂, and αβ of every othertwo-carbon-subunit of the molecule. For example, chemical structure (1)encompasses (2E, 8E)-deca-2,8-dienedioic acid (using oxylate as aloading molecule):

In some embodiments of the invention, n is an integer from 1 to 10. Insome embodiments of the invention, the even-chain diacid is adipic acid(or hexanedioc acid), suberic acid (or octanedioc acid), or sebacic acid(or decanedioc acid). In some embodiments of the invention, theeven-chain diacid is a symmetrical compound, such as a fully reducedsymmetrical aliphatic compound.

Adipic acid is a six carbon chain fully reduced symmetrical aliphaticcompound with no side chains, hence no chiral centers. Diacids of a(4+n)-configuration are synthesized from the NRPS-PKS system of thepresent invention, a four carbon succinate is extended by n extenderacyl unit(s). For example, when a six-membered chain is synthesized fromthe NRPS-PKS system of the present invention, a four carbon succinate isextended by one extender acyl unit. For example, when a ten-memberedchain is synthesized from the NRPS-PKS system of the present invention,a four carbon succinate is extended by two extender acyl units.

In some embodiments of the invention, the odd-chain diacid has thefollowing chemical structure:

wherein each R₁ and R₂ are independently H, OH, OCH₃, CH₂CH₃, or CH₃,each R₃ is independently a carbonyl, H or OH, n is an integer from 0 to10 and represents the addition of two carbons to the polyketide chain,αβ is (1) a single bond or (2) a double bond, with the proviso that whenan αβ is a double bond then the corresponding R₃ is H, and n indicatesthe number of two-carbon-chain subunits in the carbon backbone of theeven-chain diacid. Within each the odd-chain diacids, the R₁, R₂, R₃,and αβ within each two-carbon-subunit can be independent of (and so canbe identical to or different from) the R₁, R₂, R₃, and αβ of every othertwo-carbon-subunit of the molecule.

In some embodiments, the present invention provides methods for makingthe odd-chain diacid malonic acid.

In some embodiments, the present invention provides methods for makingthe odd-chain diacid pimelic acid.

Malonic acid has numerous industrial uses. Malonate esters of alkylchains from 1-20 carbons are used, for example, in the production ofcosmetics, perfumes and fragrances, barbiturates, agrochemicals,preservatives, flavoring agents, non-steroidal anti-inflammatory agents(NSAIDS), anti-depression drugs, sedatives, anesthetics, hypnotics,anticonvulsants, and paint binders. Malonic acid is also used in chickenfeed as an osteoresorptive inhibitor, as an electrolyte additive formetal anodization, to produce electroactive polymers, to producemethylidene malonates and polymers thereof, and in complex mixtures suchas Santosol® DME-1. These complex mixtures can be use as fireretardants, UV protective films, hydrophilic polymers and films,hydrophobic polymers and films, binders, sealants, and anaerobicadhesives. Diesters of malonate also have numerous uses. For example,diethylmalonate is used in perfumes as well as in the synthesis of manycompounds such as barbiturates, artificial flavorings, vitamin B1 andvitamin B6. Other diesters that can be produced in accordance with themethods of the invention include but are not limited to dimethylmalonate, dipropyl malonate, dibutyl malonate, and up to C20 alcoholsesterified to malonate.

In some embodiments, the invention results in the production of alactam. Such lactams can be comprised of C4-C16 of either even or oddchain length. Where the terms even and odd are used, they refer to thenumber of carbons in the backbone of the molecule.

By starting with the 4-carbon gamma amino butyric acid (GABA), asdescribed below, even chain lactams C4 and higher, including but notlimited to caprolactam and the C12 lactam used in engineering polymerNylon 12, can be produced. By introducing a beta-alanine loading module,such as that from the fluvirucin pathway, biosynthetic pathways thatproduced odd chain lactams, such as that used in engineering polymerNylon 11, can be generated.

In some embodiments of the invention, even chain lactams arebiosynthesized by using a loading module derived from a glycine-specificNRPS module. More than a dozen such modules have been identified thusfar in nature (see, e.g., Rausch, et al. Nucleic Acids Research, 2005,33 (18):5799-5808). PKS/NRPS hybrids are common in nature and a numberof these biosynthesis pathways have been shown to be amenable toengineering.

In some embodiments of the invention an alpha amino acid is incorporatedby the PKS/NRPS hybrid system to yield a lactam possessing a pendentside chain. For example, if a phenylalanine loading module is used in atriketide system incorporating two malonyl-CoAs and catalyzing all threepossible reductions with each extension, the output is a caprolactamderivative with a phenyl side chain. The same type of approach is usedin accordance with the methods of the invention to produce derivatizedlactams, the cognate open chain forms and diamines by appropriateselection of the NRPS loading module. With any of the described starters(loading modules), one also exploits the flexibility of PKS systems togenerate derivatives with a great variety of different oxidative statesand alkyl side chains. This flexibility applies not only to the systemsstarting with GABA, but those starting with any other amino acid.

In some embodiments of the invention the PKS or PKS/NRPS hybrid systemproduces the cognate amino acid to the described lactam. These acids canbe accessed biologically by incorporating a thioesterase that releasesthe polyketide as a free acid or by chemical hydrolysis of the lactam exvivo.

6-Aminocaproic acid is the cognate amino acid to caprolactam. It is usedto treat excessive postoperative bleeding, especially after proceduresin which a great amount of bleeding is indicated. It is marketed underthe trade name Amicar®. It is produced by ring opening of caprolactam. Abiological route for synthesis of 6-aminocaproic acid and, therefore,caprolactam, as provided by the invention, is advantageous.

In some embodiments of the invention the PKS or PKS/NRPS hybrid systemproduces a diamine. These compounds can be accessed biologically byincorporating a thioesterase and amino transferase that coordinatelyrelease and convert the final Acyl-ACP thioester to a terminal amine.

The present invention provides for a polyketide synthase (PKS) capableof synthesizing 7-keto-8-amino-pelargonic acid (KAPA). KAPA is anadvance intermediate in biotin biosynthesis. Introducing an alternativeroute to KAPA circumvents a number of regulatory check points in thebiosynthesis of biotin. Therefore, the addition of a novel KAPAbiosynthesis pathway or KAPA itself, to biotin producing organism is ameans to increasing production of this valuable chemical. The presentinvention provides for a recombinant nucleic acid that encodes apolyketide synthase (PKS) capable of synthesizing KAPA. The presentinvention provides for a host cell comprising any of the recombinantnucleic acid and/or PKS of the present invention, wherein when culturedunder a suitable condition the host cell is capable of producing KAPA,and optionally biotin. The present invention provides a method ofproducing KAPA, and optionally biotin, comprising: providing a host cellof the present invention, and culturing said host cell in a suitableculture medium such that KAPA, and optionally biotin, is produced. Thepresent invention provides for a composition comprising KAPA, andoptionally biotin, isolated from a host cell from which KAPA, andoptionally biotin, is produced, and trace residues and/or contaminantsof the host cell.

7-Keto-8-amino-pelargonic acid (KAPA) has the following structure:

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing an even-chain diacid and the PKS comprises twopolypeptide modules, wherein the first module comprises an aspartatespecific adenylation (A) domain, modified to load succinate instead ofaspartate, from the non-ribosomal peptide synthetase (NRPS) pathway forcalcium-dependent antibiotic (CDA) from Saccharopolyspora erythraealinked to a peptidylcarrier protein (PCP) domain and a second modulecomprising a PKS ketosynthase (KS) domain, wherein the PCP domain iscapable of interacting with the KS domain. In some embodiments of theinvention, the PCP domain is the PCP domain from the bleomycin pathwayfrom Streptomyces verticillus. In some embodiments of the invention, theA domain is directly linked to the PCP domain. In some embodiments ofthe invention, the second module comprises the KS domain (derived fromthe bleomycin pathway) fused to nystatin module 5, wherein theeven-chain diacid produced is adipic acid (see Example 1 and FIG. 11).In some embodiments of the invention, the modification of the A domaincomprises the conserved aspartate residue (“Asp235”) changed toglutamine.

In some embodiments of the invention ery TE is used to release freeacids from our hybrid PKS. In other embodiments this role is fulfilledby the thioesterase MonCII from the monensin pathway in Streptomycescinnamonensis, or that from the spirangein PKS.

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing an even-chain diacid and the PKS comprises theloading domain of the chondrochloren PKS wherein the CoA ligase domainof the loading domain is replaced with a succinyl-CoA synthetase, suchthe loading domain loads succinate instead of butyrate. In someembodiments, the AT specificity of the extender domain can also bechanged. Two examples are shown in FIG. 7.

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing an even-chain diacid and the PKS comprises amutant non-ribosomal peptide synthetase (NRPS) domain mutated toincorporate succinate, instead of aspartate, is used. The mutant NRPSdomain is produced by substituting the amino acid(s), including an Aspto Gln change at “Asp235” (the conserved Asp235 residue of thesubstrate-binding pocket as defined in the gramicidin S synthasephenylalanine-activating domain as identified by Challis G L, Ravel J, &Townsend C A. Chem Biol. 2000 Mar.; 7(3):211-24) a key residue involvedin the recognition of the alpha nitrogen in an aspartate-specific Adomain.

In some embodiments of the invention, the invention comprises extendingand reducing a polyketide with a pendant carboxylate group.

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing an even-chain diacid and the PKS comprises aterminal module comprising Nystatin modules 5 or 15 or the like, whichincorporate malonyl-CoA and fully reduce a corresponding β-carbonylgroup, and an Ery TE domain fused to the terminal module. (See FIG. 8.)

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing an even-chain diacid and the PKS comprises anetnangien loading module which incorporates succinate using a trans-ATdomain. The etnangien loading module is taught in Menche et al. (J. Am.Chem. Soc. (2008) 130: 14234-14243; hereby incorporated by reference).

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing an even-chain diacid and the PKS comprises amodule in which a terminal carbon is incorporated as a methyl groupwhich is later oxidized by a cytochrome P450. There are examples ofmethyl to carboxylate conversions in several of the amphipatic PKSpathways, such as for nystatin.

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing an odd-chain diacid and the PKS comprises amutant non-ribosomal peptide synthetase (NRPS) domain capable of loadingsuccinic acid.

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing lactam and the PKS comprises a non-ribosomalpeptide synthetase (NRPS) domain capable of loading glycine.

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing a diamine and the PKS comprises a non-ribosomalpeptide synthetase (NRPS) domain capable of loading glycine.

In some embodiments of the invention, the polyketide synthase (PKS) iscapable of synthesizing lactam and the PKS comprises a loading modulecapable of loading beta alanine.

In some embodiments of the invention, the polyketide synthase (PKS)comprises a NRPS loading module specific for the amino acid alaninecoupled to three PKS modules possessing all three reducing domains witha thioesterase (TE) at the C-terminus, wherein the PKS is capable ofsynthesizing 7-keto-8-amino-pelargonic acid (KAPA) (see FIG. 9).

Nucleic Acids Encoding the PKS

The present invention provides for a recombinant nucleic acid thatencodes a polyketide synthase (PKS) of the present invention. Therecombinant nucleic acid can be a double-stranded or single-strandedDNA, or RNA. The recombinant nucleic acid can encode an open readingframe (ORF) of the PKS of the present invention. The recombinant nucleicacid can also comprise promoter sequences for transcribing the ORF in asuitable host cell. The recombinant nucleic acid can also comprisesequences sufficient for having the recombinant nucleic acid stablyreplicate in a host cell. The recombinant nucleic acid can be repliconcapable of stable maintenance in a host cell. In some embodiments, thereplicon is stably integrated into a chromosome of the host cell. Insome embodiments, the replicon is a plasmid. The present invention alsoprovides for a vector or expression vector comprising a recombinantnucleic acid of the present invention. The present invention providesfor a host cell comprising any of the recombinant nucleic acid and/orPKS of the present invention. In some embodiments, the host cell, whencultured under a suitable condition, is capable of producing theeven-chain or odd-chain diacid, or lactam, or diamine.

The large number of polyketide pathways that have been elucidatedprovide many different options to produce diacids, lactams, and diaminesas well as the large number of derivatives in accordance with themethods of the invention. While the products can be different in sizeand functionality, all employ the methods of the invention forbiosynthesis. The interfaces between non-cognate enzyme partners can bedetermined for preparing the hybrid synthase. ACP-linker-KS andACP-linker-TE regions from the proteins of interest are aligned toexamine the least disruptive fusion point for the hybrid synthase.Genetic constructions will employ one of several standard sequence andligation independent cloning method so as to eliminate the incorporationof genetic “scarring”.

It will be apparent to one of skill in the art that a variety ofrecombinant vectors can be utilized in the practice of aspects of theinvention. As used herein, “vector” refers to polynucleotide elementsthat are used to introduce recombinant nucleic acid into cells foreither expression or replication. Selection and use of such vehicles isroutine in the art. An “expression vector” includes vectors capable ofexpressing DNAs that are operatively linked with regulatory sequences,such as promoter regions. Thus, an expression vector refers to arecombinant DNA or RNA construct, such as a plasmid, a phage,recombinant virus or other vector that, upon introduction into anappropriate host cell, results in expression of the cloned DNA.Appropriate expression vectors are well known to those of skill in theart and include those that are replicable in eukaryotic cells and/orprokaryotic cells and those that remain episomal or those that integrateinto the host cell genome.

The vectors may be chosen to contain control sequences operably linkedto the resulting coding sequences in a manner that expression of thecoding sequences may be effected in an appropriate host. Suitablecontrol sequences include those that function in eukaryotic andprokaryotic host cells. If the cloning vectors employed to obtain PKSgenes encoding derived PKS lack control sequences for expressionoperably linked to the encoding nucleotide sequences, the nucleotidesequences are inserted into appropriate expression vectors. This can bedone individually, or using a pool of isolated encoding nucleotidesequences, which can be inserted into host vectors, the resultingvectors transformed or transfected into host cells, and the resultingcells plated out into individual colonies. Suitable control sequencesfor single cell cultures of various types of organisms are well known inthe art. Control systems for expression in suitable host cells, such asyeast and prokaryotic host cells, are widely available and are routinelyused. Control elements include promoters, optionally containing operatorsequences, and other elements depending on the nature of the host, suchas ribosome binding sites. Particularly useful promoters for prokaryotichosts include those from PKS gene clusters that result in the productionof polyketides as secondary metabolites, including those from Type I oraromatic (Type II) PKS gene clusters. Examples are act promoters, tcmpromoters, spiramycin promoters, and the like. However, other bacterialpromoters, such as those derived from sugar metabolizing enzymes, suchas galactose, lactose (lac) and maltose, are also useful. Additionalexamples include promoters derived from biosynthetic enzymes such as fortryptophan (trp), the β-lactamase (bla), bacteriophage lambda PL, andT5. In addition, synthetic promoters, such as the tac promoter (U.S.Pat. No. 4,551,433; hereby incorporated by reference), can be used.

As noted, particularly useful control sequences are those whichthemselves, or with suitable regulatory systems, activate expressionduring transition from growth to stationary phase in the vegetativemycelium. Illustrative control sequences, vectors, and host cells ofthese types include the modified S. coelicolor CH999 and vectorsdescribed in PCT publication no. WO 96/40968 and similar strains of S.lividans. See U.S. Pat. Nos. 5,672,491; 5,830,750; 5,843,718; and6,177,262, each of which is hereby incorporated by reference. Otherregulatory sequences may also be desirable which allow for regulation ofexpression of the PKS sequences relative to the growth of the host cell.Regulatory sequences are known to those of skill in the art, andexamples include those which cause the expression of a gene to be turnedon or off in response to a chemical or physical stimulus, including thepresence of a regulatory compound. Other types of regulatory elementsmay also be present in the vector, for example, enhancer sequences.

Selectable markers can also be included in the recombinant expressionvectors. A variety of markers are known which are useful in selectingfor transformed cell lines and generally comprise a gene whoseexpression confers a selectable phenotype on transformed cells when thecells are grown in an appropriate selective medium. Such markersinclude, for example, genes that confer antibiotic resistance orsensitivity to the plasmid.

The various PKS nucleotide sequences, or a mixture of such sequences,can be cloned into one or more recombinant vectors as individualcassettes, with separate control elements or under the control of asingle promoter. The PKS subunits or components can include flankingrestriction sites to allow for the easy deletion and insertion of otherPKS subunits. The design of such restriction sites is known to those ofskill in the art and can be accomplished using the techniques describedabove, such as site-directed mutagenesis and PCR. Methods forintroducing the recombinant vectors of the present invention intosuitable hosts are known to those of skill in the art and typicallyinclude the use of CaCl₂ or other agents, such as divalent cations,lipofection, DMSO, protoplast transformation, conjugation, andelectroporation.

Host Cells Comprising the PKS

The present invention provides for a host cell comprising any of therecombinant nucleic acid and/or PKS of the present invention. In someembodiments, the host cell, when cultured, is capable of producing aneven-chain or odd-chain diacid, or lactam, or diamine. The host cell canbe a eukaryotic or a prokaryotic cell. Suitable eukaryotic cells includeyeast cells, such as from the genus Saccharomyces orSchizosaccharomyces. A suitable species from the genus Saccharomyces isSaccharomyces cerevisiae. A suitable species from the genusSchizosaccharomyces is Schizosaccharomyces pombe. Suitable prokaryoticcells include Escherichia coli, Bacillus or Streptomyces species.

The PKS can be in a host cell, or isolated or purified. The PKS cansynthesize the even-chain or odd-chain diacid, or lactam, or diamine invivo (in a host cell) or in vitro (in a cell extract or where allnecessary chemical components or starting materials are provided). Thepresent invention provides methods of producing the even-chain orodd-chain diacid, or lactam, or diamine using any of these in vivo or invitro means.

In some embodiments of the invention, the host cell comprises a PKS ofthe present invention capable of producing pimelic acid, and furthercomprises the enzymes pimelyl-CoA synthetase, 8-amino-7-oxononanoatesynthase, 7,8-diamino-pelargonic acid (DAPA) synthase, dethiobiotinsynthase, and biotin synthase, and/or one or more nucleic acids encodingpimelyl-CoA synthetase, 8-amino-7-oxononanoate synthase, DAPA synthase,dethiobiotin synthase, and biotin synthase, or functional variantsthereof. When the host cell is cultured under a suitable condition, thehost cell is capable of expressing or producing pimelyl-CoA synthetase,8-amino-7-oxononanoate synthase, DAPA synthase, dethiobiotin synthase,and biotin synthase, or functional variants thereof, which in turn arecapable of converting pimelic acid into biotin (or Vitamin H).

In some embodiments of the invention, the host cell comprises a PKS ofthe present invention capable of producing KAPA, and further comprisesthe enzymes 7,8-diamino-pelargonic acid (DAPA) synthase, dethiobiotinsynthase, and biotin synthase, or functional variants thereof, and/orone or more nucleic acids encoding DAPA synthase, dethiobiotin synthase,and biotin synthase, or functional variants thereof. When the host cellis cultured under a suitable condition, the host cell is capable ofexpressing or producing DAPA synthase, dethiobiotin synthase, and biotinsynthase, or functional variants thereof, which in turn are capable ofconverting KAPA into biotin (or Vitamin H).

Examples of suitable pimelyl-CoA synthetase are the gene productsencoded by the bio W genes of Bacillus subtilus, and Bacillussphearicus. An illustrative amino acid sequence, of B. subtiluspimelyl-CoA synthetase (GenBank Accession No.: AAC00261), comprises:

  1 mngshedggk hisggerlip fhemkhtvna llekglshsr gkpdfmqiqf eevhesikti 61 qplpvhtnev scpeegqkla rlllekegvs rdviekayeq ipewsdvrga vlfdihtgkr121 mdqtkekgvr vsrmdwpdan fekwalhshv pahsrikeal alaskvsrhp avvaelcwsd181 dpdyitgyva gkkmgyqrit amkeygteeg crvffidgsn dvntyihdle kqpiliewee241 dhds (SEQ ID NO: 1)

Examples of suitable 8-amino-7-oxononanoate synthase are the geneproducts encoded by the bioF genes of E. coli, B. subtilus, and B.sphearicus. An illustrative amino acid sequence, of E. coli8-amino-7-oxononanoate synthase (GenBank Accession No.: AP_001407),comprises:

  1 mswqekinaa ldarraadal rrrypvagga grwlvaddrq ylnfssndyl glshhpqiir 61 awqqgaeqfg igsggsghvs gysvvhqale eelaewlgys rallfisgfa anqaviaamm121 akedriaadr lshaslleaa slspsqlrrf ahndvthlar llaspcpgqq mvvtegvfsm181 dgdsaplaei qqvtqqhngw lmvddahgtg vigeqgrgsc wlqkvkpell vvtfgkgfgv241 sgaavlcsst vadyllqfar hliystsmpp aqaqalrasl avirsdegda rreklaalit301 rfragvqdlp ftladscsai qplivgdnsr alqlaeklrq qgcwvtairp ptvpagtarl361 rltltaahem qdidrllevl hgng (SEQ ID NO: 2)

Examples of suitable DAPA synthases are BIO3 of S. cerevisae, and thegene product encoded by the bioA genes of E. coli, B. subtilus, and B.sphearicus. An illustrative amino acid sequence, of E. coli DAPAsynthase (GenBank Accession No.: AP_001405), comprises:

  1 mttddlafdq rhiwhpytsm tsplpvypvv saegcelils dgrrlvdgms swwaaihgyn 61 hpqlnaamks qidamshvmf ggithapaie lcrklvamtp qplecvflad sgsvavevam121 kmalqywqak gearqrfltf rngyhgdtfg amsvcdpdns mhslwkgylp enlfapapqs181 rmdgewderd mvgfarlmaa hrheiaavii epivqgaggm rmyhpewlkr irkicdregi241 lliadeiatg fgrtgklfac ehaeiapdil clgkaltggt mtlsatlttr evaetisnge301 agcfmhgptf mgnplacaaa naslailesg dwqqqvadie vqlreqlapa rdaemvadvr361 vlgaigvvet thpvnmaalq kffveqgvwi rpfgkliylm ppyiilpqql qrltaavnra421 vqdetffcq (SEQ ID NO: 3)

Examples of suitable dethiobiotin synthases are BIO4 of S. cerevisae,and the gene product encoded by the bioD genes of E. coli, B. subtilus,and B. sphearicus. An illustrative amino acid sequence, of E. colidethiobiotin synthase (GenBank Accession No.: CAA00967), comprises:

  1 mskryfvtgt dtevgktvas callqaakaa gyrtagykpv asgsektpeg lrnsdalalq 61 rnsslqldya tvnpytfaep tsphiisaqe grpieslvms aglralehka dwvlvegagg121 wftplsdtft fadwvtqeql pvilvvgvkl gcinhamlta qviqhagltl agwvandvtp181 pgkrhaeymt tltrmipapl lgeipwlaen penaatgkyi nlall (SEQ ID NO: 4)

Examples of suitable biotin synthases are BIO2 of S. cerevisae, and thegene product encoded by the bioB genes of E. coli, B. subtilus, and B.sphearicus. An illustrative amino acid sequence, of E. coli biotinsynthase (Gen Bank Accession No.: AP_001406), comprises:

  1 mahrprwtls qvtelfekpl ldllfeaqqv hrqhfdprqv qvstllsikt gacpedckyc 61 pqssryktgl eaerlmeveq vlesarkaka agstrfcmga awknpherdm pyleqmvqgv121 kamgleacmt lgtlsesqaq rlanagldyy nhnldtspef ygniittrty qerldtlekv181 rdagikvcsg givglgetvk draglllqla nlptppesvp inmlvkvkgt pladnddvda241 fdfirtiava rimmptsyvr lsagreqmne qtqamcfmag ansifygckl lttpnpeedk301 dlqlfrklgl npqqtavlag dneqqqrleq almtpdtdey ynaaal (SEQ ID NO: 5)Methods of Using the PKS

The present invention provides a method of producing an even-chain orodd-chain diacid, or lactam, or diamine comprising: providing a hostcell of the present invention, and culturing said host cell in asuitable culture medium such that the even-chain or odd-chain diacid, orlactam, or diamine is produced. The method can further compriseisolating said even-chain or odd-chain diacid, or lactam, or diaminefrom the host cell and the culture medium. The method can furthercomprise reacting the even-chain or odd-chain diacid with a diamine toproduce a nylon. The method can also comprise the polymerization of thelactams, or cognate amino acids. A suitable diamine is an alkanediamine, such as hexane-1,6-diamine. Alternatively, the method canfurther comprise reacting the even-chain or odd-chain diacid with adialcohol to produce a polyester. A suitable dialcohol is an alkanediol, such as ethylene glycol, propane diol, or butanediol. A variety ofmethods for heterologous expression of PKS genes and host cells suitablefor expression of these genes and production of polyketides aredescribed, for example, in U.S. Pat. Nos. 5,843,718; 5,830,750 and6,262,340; WO 01/31035, WO 01/27306, and WO 02/068613; and U.S. PatentApplication Pub. Nos. 20020192767 and 20020045220; hereby incorporatedby reference.

The present invention provides for a composition comprising aneven-chain or odd-chain diacid, or lactam, or diamine isolated from ahost cell from which the even-chain or odd-chain diacid, or lactam, ordiamine is produced, and trace residues and/or contaminants of the hostcell. Such trace residues and/or contaminants include cellular materialproduced by the lysis of the host cell.

The even-chain diacids, such as adipic acid, or odd-chain diacids, orlactam, or diamine, provide for the production of “green” nylon, such asthat used in Mohawk carpet fibers. Besides nylon production, the abilityto manipulate the side chains of the even-chain or odd-chain diacids, orlactams, or diamines provides for the production of novel polymerprecursors that would lead to polymers with a variety of properties.These products may also serve as adhesive, lubricants or precursors forpharmaceuticals or other more complicated compounds.

Producing Biotin

The present invention provides for a method of producing biotin,comprising: providing a host cell comprising one or more nucleic acidsencoding and capable of expressing or producing a PKS capable ofproducing pimelic acid, and pimelyl-CoA synthetase,8-amino-7-oxononanoate synthase, DAPA synthase, dethiobiotin synthase,and biotin synthase, and culturing said host cell in a suitable culturemedium such that biotin is produced. A variety of methods forheterologous expression of these genes and host cells suitable forexpression of these genes and production of polyketides are describedherein. A hybrid PKS capable of producing pimelic acid is taught in U.S.Patent Application Ser. No. 61/040,583, PCT International PatentApplication PCT/US2009/038831, and U.S. patent application Ser. No.12/922,204, which are incorporated by reference.

The present invention provides for a method of producing biotin,comprising: providing a host cell comprising one or more nucleic acidsencoding and capable of expressing or producing a PKS capable ofproducing KAPA, and DAPA synthase, dethiobiotin synthase, and biotinsynthase, and culturing said host cell in a suitable culture medium suchthat biotin is produced. A variety of methods for heterologousexpression of these genes and host cells suitable for expression ofthese genes and production of polyketides are described herein.

The method can further comprise isolating said biotin from the host celland the culture medium. The method can further comprise administeringthe isolated biotin to a human or animal in need of or suspected to bein need of biotin. In some embodiments, the administering comprises thehuman or animal orally ingesting the biotin.

The present invention provides for a composition comprising biotinisolated from a host cell from which the biotin is produced, and traceresidues and/or contaminants of the host cell. Such trace residuesand/or contaminants include cellular material produced by the lysis ofthe host cell. The biotin isolated is useful for nutritional purposes.The type and amount of the trace residues and/or contaminants isolatedwith the biotin is not harmful to the health of a human or animal orallyingesting the biotin.

The present invention has one or more of the following advantages: (1)it reduces the dependence on oil for producing certain chemicals, and(2) it serves as a means of capture and sequestration of carbon from theatmosphere.

The invention having been described, the following examples are offeredto illustrate the subject invention by way of illustration, not by wayof limitation.

In the examples below, reference is made to either DNA or proteinsequence present in the NCBI data that is used to produce the enzymesrequired to make the products described. It is understood that theprotein sequences can be back-translated to produce DNA segments ofpreferred codon usage, or that the DNA sequences present in databasescan be used directly or changed to correspond to the same proteinsequence with preferred codon usage.

EXAMPLE 1 Production of Adipic Acid Using a Mutated NRPS A Domain

The production of adipic acid is achieved by coupling an aspartatespecific A domain from the non-ribosomal peptide synthetase (NRPS)pathway for calcium-dependent antibiotic (CDA) from Saccharopolysporaerythraea to a peptidylcarrier protein (PCP) domain from bleomycinpathway from Streptomyces verticillus. This PCP is chosen because itnatively interacts with a PKS ketosynthase (KS) domain. The chimericprotein is designated AAS1 (adipic acid synthase ORF 1). As a second ORF(aas2), this KS domain (bleomycin PKS) is fused to nystatin module 5which was previously fused to the thioesterase (TE) domain from theerythromycin pathway. The two enzymes and their catalytic domains areillustrated in FIG. 11. In order to change the specificity of theadenylation domain from the CDA pathway, the amino acid loading domainis mutated at a conserved aspartate residue (“Asp235”) that is known tostabilize the alpha-amino side chain of the natively loaded amino acid.By blocking this interaction we sought to change the specificity fromaspartate to the des-amino form of the same molecule, succinate. Asaturation mutagenesis library is made at this position of the A domain.Each of the 20 versions of this enzyme were carried on the backbonepBbA7c and were co-transformed into E. coli BAP-1, grown to a sufficientoptical density (OD), such as ˜0.4, induced and analyzed by LC-MS. Theconstruct carrying an Asp to Gln mutation at “Asp235” showed adipic acidproduction (Table 2).

TABLE 2 Samples labeled UI are uninduced, those labeled are inducedcultures. I9 was lost. UI6 carries an Asp to Gln mutation at “Asp235”.Sample name Area uM mg/L UI 1 0 0 0 UI 2 0 0 0 UI 3 0 0 0 UI 4 0 0 0 UI5 0 0 0 UI 6 42,671 1.56 0.23 UI 7 0 0 0 UI 8 0 0 0 UI 9 0 0 0 UI 10 0 00 UI 11 0 0 0 UI 12 0 0 0 UI 13 0 0 0 UI 14 0 0 0 UI 15 0 0 0 UI 16 0 00 UI 17 0 0 0 UI 18 0 0 0 UI 19 0 0 0 UI 20 0 0 0 I 1 0 0 0 I 2 0 0 0 I3 0 0 0 I 4 0 0 0 I 5 0 0 0 I 6 0 0 0 I 7 0 0 0 I 8 0 0 0 I 9 0 0 0 I 100 0 0 I 11 0 0 0 I 12 0 0 0 I 13 0 0 0 I 14 0 0 0 I 15 0 0 0 I 16 0 0 0I 17 0 0 0 I 18 0 0 0 I 19 0 0 0 I 20 0 0 0

EXAMPLE 2 Production of Even-chain Diacids Using the SpirofunginBiosynthesis Genes

Spirofungin A (FIG. 12-1) is a dicarboxylic acid composed of twenty-fourcarbons in its polyketide backbone that is organized into a spiroketalsub-structure. It is produced by the bacterium Streptomycesviolaceusniger Tü 4113. Reveromycin (FIG. 12-2), produced fromStreptomyces sp. SN-593 has a similar backbone and spiroketalsubstructure but differs from spirofungin in the atoms shown in blue.

Sequencing of the corresponding genes involved in the biosynthesis ofthe two compounds indicated that the polyketide is produced with a27-carbon backbone by a type I polyketide synthase and then subsequentlyreleased and processed into the 24-carbon atom backbone containing anacid group at each end. Through analysis and comparison of the sequencesof the genes flanking the PKS in both organisms, we have identified thepathway for the production of that converts the final acyl-ACPintermediate of spirofungin in module 12 of the spirofungin PKS tospirofungin A (FIG. 13).

The PKS consists of 12 modules and determines the biosynthesis of anacyl intermediate with 27 carbons in its chain. As shown in FIG. 13, theacyl chain contains an OH group at C-25 (C-1 is attached to the S atomcovalently associated with the ACP domain). The thioesterse (TE) domainof module 12 releases the acyl chain either as a free acid at C-1 or asa 26-member macrolactone which is formed between C-1 and the OH at C25.This compound is then converted to the free intermediate designated“prespirofungin” through the action of the following enzymes: (1) Anesterase (EST) that opens the lactone. The gene determining the esteraseactivity is designated ORF1 in the spirofungin cluster. (2) An alcoholdehydrogenase-like enzyme (ADH) that converts the 25-OH to itscorresponding ketone. ADH is determined by ORF7 in the spirofungincluster. (3) A flavin-binding family monooxygenase (FMO) that attacksC24, breaking the C24-C25 bond releasing the free acid (prespirofungin)and propionaldehyde. FMO is determined by ORF4. (4) An aldehydedehydrogenase (ALDH) that converts propionaldehyde to propionic acid.ALDH is determined by ORF6. Prespirofungin is converted to spirofungin Athrough the action of additional enzymes determined by genes in thespirofungin biosynthesis cluster that form the spiroketal sub-structure.

It is possible that the spiroketal sub-structure is formed before theacyl end is converted to the acidic group, either while the acyl chainis tethered to the ACP of module 12, or immediately after it is releasedby the thioesterase (and opened from its macrolactam structure by theesterase (SpiN). The acid group is then formed by the action of SpiE,SpiH, and SpiF as described above. Similarly, the acid group at C24 ofreveromycin is formed by the action of similar enzymes EST (RevN), ADH(RevE), FMO (RevH), and ALDH (RevF).

An approach to produce adipic acid is shown in FIG. 14. The PKS iscomposed of a loading module and three extension modules with thedomains indicated. The PKS produces the intermediates [a], [b], [c] and[d], each attached to the ACP domain at the end of the biochemicalprocesses in the load module and modules 1-3, respectively. Compound dconsists of a 9-carbon backbone that is released from the ACP by the TEdomain and converted to the 6-carbon diacid, adipic acid, and propionicacid by the action of the enzymes EST, ADH, FMO and ALDH, which areproduced from expression of the genes spiN, spiE, spiH, and spiF fromthe spirofungin gene cluster from Streptomyces violaceusniger Tü 4113(see, the www site ncbi.nlm.nih.gov/nuccore/CP002994.1: Spirofungincluster: Strvi_6572-Strvi_6584), or the corresponding genes revN, revE,revH, and revF from the reveromycin gene cluster from Streptomyces sp.SN-593 (NCBI Accession No. AB568601).

EXAMPLE 3 Production of Even-chain Diacids Using the Succinyl CoA Ligase

Succinyl CoA Ligase. The recent publication of the chondrochlorenbiosynthesis cluster shows a loading domain that consists of a CoAligase and ACP domain (Rachid et al., “Unusual chemistry in thebiosynthesis of the antibiotic chondrochlorens,” Biology & Chemistry16:70-81, 2009; hereby incorporated by reference). The native systemloads a four-carbon butyrate, extends with methylmalonate and fullyreduces the β-carbonyl (FIG. 4). The addition of a thioesterase domain(DEBS-TE) catalyzes the release of 2-methylhexanoic acid (FIG. 10).

Replacement of the CoA ligase domain with a succinyl-CoA synthetaseallows the loading of succinate. There are a number of succinyl-CoAligases. All appear to function as heterodimers or α2β2 tetramers. Theyall carry the 5 conserved domains illustrated in FIG. 6. Because wedesire to load succinate onto the phosphopantetheinyl arm of the ACPrather than the phosphopantetheinyl arm of CoA, we should be able toeliminate domain 1. An adhesion domain could be added to the N-terminusof the ACP and another to part of the succinyl-CoA synthetase complex.These would be co-expressed with a scaffold protein to link themtogether. The obvious question lies in the placement of the adhesion onthe CoA-synthetase. This will have to be done in such a way that theactive site is oriented toward the phosphopantetheinyl arm of the ACP.

This combined with the addition of the TE domain would facilitate theproduction of 2-methyl-hexanedioic acid (FIG. 7A). Finally, the nativeCndA enzyme loads a methylmalonate extender unit. One can change the ATspecificity (which has been done successfully via targeted mutagenesisof a few residues) or couple the loading domain to a module containing amalonate loading AT and all three reducing domains, such as Nys-mod5.The result in introducing all of these modifications would be a minimalPKS system that produces adipic acid (FIG. 7B).

EXAMPLE 4 Production of Even-chain Diacids Using the Etnangien LoadingModule

Etnangien is a macrolide-polyene antibiotic produced from Sorangiumcellulosum that is composed of a macrocylic ring and a long polyketidechain that terminates with a carboxylate group. The beginning steps ofthe biosynthesis of the etnangien is shown in FIG. 15. Succinyl-CoA isloaded on the ACP1 domain of module 1 using a discrete (trans) AT enzymeencoded by EtnB or EtnK to produce succinyl-ACP (FIG. 15[a]) Similarly,malonyl-CoA is loaded on ACP2 or ACP3 of module 1 by EtnB or EtnK(malonyl-ACP not shown). The KS domain of module 1 creates thethioesterintermediate 3-oxo-5-carboxypentanoyl-ACP (not shown). The 3-oxo groupis then attacked by a β-methylation enzyme system, ECH1 and ECH2 thatadds a methyl group at C-3 and leaves the 2,3-bond unsaturated resultingin intermediate 3-methyl-5-carboxy-[2,3]pentenoyl-ACP (FIG. 15[b]). Thisacyl-intermediate is used for the next round of polyketide synthesis toyield compound c (FIG. 15[c]).

Production of Adipic Acid—Two strategies are used to produce adipic acidemploying components of the etnangien PKS. In the first, (FIG. 16), achimeric PKS employs the segment of the etnangien PKS in the gene etnDcontaining the entire sequence of module 1 from Sorangium cellulosum(NCBI Accession No. YP001613827), and a segment from a second PKS thatencodes the DH-ER-KR domains introduced between the ACP2 and ACP3. Thesedomains are available as a contiguous segment from numerous PKSs,including but not limited to module 4 of the erythromycin PKS fromSaccharopolyspora erythraea (NCBI Accession No. M63677.1), module 4 ofthe pikromycin PKS from Streptomyces venezuelae (NCBI Accession No.BD232534.1), or modules 7 or 12 of the oligomycin PKS from Streptomycesavermitilis (NCBI Accession No. NC_003155). The genes for EtnB and EtnKfrom Sorangium cellulosum (NCBI Accession Nos. YP001613825 andYP001613834, respectively) are also introduced into the host to producethe corresponding trans AT enzymes to ensure that both succinyl-ACP1 andmalonyl-ACP2 are formed. The KS domain acts to form the 6 carbondiketide that is then reduced to adipyl-ACP by the KR, DH and ER domainsand released by the TE domain to yield adipic acid. Examples of TEdomains include, but are not limited to, the TE domain from theniddamycin PKS from Streptomyces caelestis (NCBI Accession No.AF016585), the oligomycin PKS from Streptomyces avermitilis (NCBIAccession No. NC_003155), the epothilone PKS from Sorangium cellulosum(NCBI Accession No. AF217189), the pikromycin PKS from Streptomycesvenezuelae (NCBI Accession No. BD232534), and the erythromycin PKS fromSaccharopolyspora erythraea (NCBI Accession No. M63677.1).

In a second embodiment employing the etnangien PKS components, achimeric PKS is constructed as a single ORF employing, as shown in FIG.17, DNA segments corresponding to the inactivated KS and ACP1 domainsfrom module 1 of EtnD linked to the KS domain of module 2 from Sorangiumcellulosum (NCBI Accession No. YP001613287) linked to a DNA segmentcontaining malonyl-specific AT domain and the DH-ER-KR-ACP domainslinked to a TE domain. Inactivation of the KS domain is accomplished bydeleting all or most of the KS domain without disrupting the readingframe. Examples of AT-DH-ER-KR-ACP segments that can be used in thisconstruct include, but are not limited to the AT-DH-ER-KR-ACP segmentsfrom module 3 of the oligomycin PKS from Streptomyces avermitilis (NCBIAccession No. NC_003155), or modules 5 or 15 of the nystatin PKS fromStreptomyces noursei (NCBI Accession No. AF263912). Examples of TEdomains include, but are not limited to, the TE domain from theniddamycin PKS from Streptomyces caelestis (NCBI Accession No.AF016585), the oligomycin PKS from Streptomyces avermitilis (NCBIAccession No. NC 003155), the epothilone PKS from Sorangium cellulosum(NCBI Accession No. AF217189), the pikromycin PKS from Streptomycesvenezuelae (NCBI Accession No. BD232534.1), and the erythromycin PKSfrom Saccharopolyspora erythraea (NCBI Accession No. M63677.1).

EXAMPLE 5 Employing an AMP-ligase-PCP Didomain as the Loading Module

The scheme for production of adipic acid employing an AMP ligase-PCPdidomain to load succinic acid directly to the PKS is shown in FIG. 11.The A domain is a variant of the protein DhbE from Bacillus subtilis(NCBI Accession No. NP_391078). DhbE normally transfers dihydroxybenzoicacid to its cognate PCP, DhbB (NCBI Accession No. NP_391077). In theconstruct shown in FIG. 11, the Load Module consists of the A domainwhich is composed of DhbE*, a variant of DbhE containing the followingamino acid substitutions: S240G, V329A, and V337K, and the PCP domainconsisting of amino acids 188-312 of DhbB. The KS domain of module 1 isthe KS domain of the borrelidin PKS from Streptomyces parvulus (NCBIAccession No. ABS90475). The AT-TE segment of the PKS is as shown inFIG. 17. Examples of AT-DH-ER-KR-ACP segments that can be used in thisconstruct include, but are not limited to the AT-DH-ER-KR-ACP segmentsfrom module 3 of the oligomycin PKS from Streptomyces avermitilis (NCBIAccession No. NC_003155), or modules 5 or 15 of the nystatin PKS fromStreptomyces noursei (NCBI Accession No. AF263912). Examples of TEdomains include, but are not limited to, the TE domain from theniddamycin PKS from Streptomyces caelestis (NCBI Accession No.AF016585), the oligomycin PKS from Streptomyces avermitilis (NCBIAccession No. NC_003155), the epothilone PKS from Sorangium cellulosum(NCBI Accession No. AF217189), the pikromycin PKS from Streptomycesvenezuelae (NCBI Accession No. BD232534.1), and the erythromycin PKSfrom Saccharopolyspora erythraea (NCBI Accession No. M63677.1).

EXAMPLE 6 Production of Malonic Acid Using PKS

As shown in FIG. 18, a single, three domain, chimeric PKS module thathas a malonyl-specific acyltransferase (mAT) domain linked to itscognate ACP domain linked to a type I thioesterase (TE) domain will bindmalonyl-CoA and release malonic acid. Malonyl-CoA is naturally presentin all hosts, and is the substrate for the biosynthesis of fatty acidsin prokaryotes and fatty acids and cholesterol or its analogs (e.g.ergosterol) in eukaryotes. Malonyl-CoA is readily produced fromacetyl-CoA which is the primary degradation product of glucosemetabolism. High titers of intracellular malonyl-CoA has been achievedin both prokaryotes and eukaryotes.

Numerous PKS load modules contain the cognate mAT-ACP didomains.Examples include, but are not limited to, the AT-ACP didomain from theload module from the chalcomycin PKS from Streptomyces bikiniensis (NCBIAccession No. AY509120), the niddamycin PKS from Streptomyces caelestis(NCBI Accession No. AF016585), the oligomycin PKS from Streptomycesavermitilis (NCBI Accession No. NC_003155), and the epothilone PKS fromSorangium cellulosum (NCBI Accession No. AF217189). Numerous PKSs alsoeach contain a TE domain, any of which can be used in the assembly ofthe chimeric PKS herein. Examples include, but are not limited to, theTE domain from the niddamycin PKS from Streptomyces caelestis (NCBIAccession No. AF016585), the oligomycin PKS from Streptomycesavermitilis (NCBI Accession No. NC_003155), the epothilone PKS fromSorangium cellulosum (NCBI Accession No. AF217189), the pikromycin PKSfrom Streptomyces venezuelae (NCBI Accession No. BD232534.1), and theerythromycin PKS from Saccharopolyspora erythraea (NCBI Accession No.M63677.1). The mAT-ACP didomain or the TE domain can be cloned from thecorresponding host organism or synthesized de novo employing thepreferred codon usage for the ultimate malonic acid production host. Thesequences separating the TE domain from its adjacent ACP domain innumerous PKSs is well understood, hence it is possible to synthesize denovo, or assemble from disparate sources, the complete mAT-ACP-TEchimeric module.

EXAMPLE 7 Production of Malonic Acid Using PKS+TEII

In this embodiment, the PKS module consists of a mAT-ACP didomain thatloads malonyl-CoA and a separate type II thioesterase (TEII) that isspecific for removing the CoASH moiety from short chain acyl-CoAthioesters to produce short chain acids (FIG. 19). Examples of mAT-ACPdidomains include, but are not limited to, the AT-ACP didomain from theload module from the spiramycin, carbomycin, niddamycin, oligomycin, orepothilone PKS. The DNA segments encoding these didomains can be clonedfrom their respective natural hosts, or synthesized de novo employingemploying preferred codon usage to enhance expression in the organismchosen for malonic acid production.

Examples of TEII enzymes include TEII proteins from genes involved inthe biosynthesis of known polyketides, including, but not limited to,EryH from Saccharopolyspora erythraea (NCBI Accession No. M54983.1),MegH from Micromonospora megalomiceae (NCBI Accession No. AF2623245.1),GrsT from Streptomyces bikiniensis (NCBI Accession No. AY509120.1), orMonCII from Streptomyces cinnamonensis (NCBI Accession No. AF440781.1),from gene clusters involved in the biosynthesis of erythromycin,megalomicin, chalcomycin, and monensin, respectively. Other examples ofTEII enzymes include the family of TesB-like enzymes from a variety ofGram-negative bacteria including, but not limited to, Escherichia coli(NCBI Accession No. ZP_003256460.1), Shigella flexneri (NCBI AccessionNo. NP_706346.2), Salmonella enterica (NCBI Accession No.ZP_02656512.1), or Klebsiella pneumonia (NCBI Accession No.ZP_06015648.1), or Gram positive bacteria including, but not limited to,Brucella abortus (NCBI Accession No. YP222547.1), Agrobacteriumtumefaciens (NCBI Accession No. EGP58265.1), Brevibacterium linens (NCBIAccession No. ZP05914544.1), or Micrococcus luteus (NCBI Accession No.YP0029570745.1). The corresponding genes can be cloned from their nativehosts or synthesized de novo employing preferred codon usage to enhanceexpression in the organism chosen for malonic acid production.

In this embodiment, the mAT-ACP didomain and TEII would be expressed asseparate proteins either as part of an operon driven from a singlepromoter, or driven from separate promoters from either a singleplasmid, two plasmids, a plasmid and the chromosome or from thechromosome exclusively. To enhance the overall rate of release ofmalonyl-CoA from the mAT-ACP didomain, genes for two or more TEIIenzymes can be co-expressed in the host expressing the gene for themAT-ACP didomain.

EXAMPLE 8 Production of Malonic Acid Using Trans-AT PKS

In another embodiment of this invention, the malonate producing PKSutilizes a “trans AT” PKS system (FIG. 20). Because all known trans ATPKSs utilize malonate, any of these ACPs can be coupled to a TE, so longas the upstream portions of the PKS responsible for dimerization andtrans-AT recognition are retained. Example PKS sources for these domainsare the mupirocin, bryostatin, leinamycin, and onnamide pathways. Athioesterase suitable for releasing a free carboxylate from the ACPthioester can be utilized in this system. Examples include the DEBS,spirangein, and kalamanticin PKSs. The KS* pictured in FIG. 20 indicatesthat this domain is catalytically inactive, but included for structuralreasons.

EXAMPLE 9 Production of Caprolactam Using a PKS

Biosynthesis of caprolactam requires the synthesis of anamino-containing molecule that can start the biosynthesis of apolyketide chain on a PKS system. In the embodiment shown in FIG. 21,the starter is 4-aminobutyryl-CoA which is produced from the commonlyavailable amino acid L-argininine by enzymes designated Orf28, Orf33 andOrf27 from Streptomyces aizunensis (NCBI Accession No. AAX98201,AAX98208, AAX98202, respectively). Production of the pathway fromarginine to 4-aminobutyryl-CoA is accomplished through the synthesis ofDNA segments with the preferred codon usage corresponding to the proteinsequences of Orf26, Orf33, and Orf27 from. 4-Aminobutyryl-CoA istransferred to the Load ACP domain of the PKS shown in FIG. 21 by thetrans AT (Orf18) from Streptomyces aizunensis (NCBI Accession No.AAX98193) to yield the intermediate 4-aminobutyryl-ACP [a]. Intermediatea is extended by the PKS module 1 to produce the intermediate6-aminohexanoyl-ACP [b]. The KS domain of module 1 corresponds to the KSdomain of module 1 of the linearmycin PKS and is, hence, the naturaldomain that interacts with the Load ACP protein and to which thestarting 4-aminobutyryl moiety is transferred during native linearmycinbiosynthesis. The Load ACP through KS1 domain comes from the linearmycinPKS from Streptomyces aizunensis (NCBI Accession No. AAX98191). ThemAT-DH-ER-KR-ACP segment of module I of FIG. 21 can be taken from anumber of PKS systems. Examples include, but are not limited to themAT-DH-ER-KR-ACP containing segment from module 22 of the linearmycinPKS from Streptomyces aizunensis, (NCBI database Accession No.AAX98191), module 3 of the oligomycin PKS from Streptomyces avermitilis(NCBI Accession No. NC_003155), or modules 5 or 15 of the nystatin PKSfrom Streptomyces noursei (NCBI Accession No. AF263912). Preferred TEdomains shown in FIG. 21 that both releases and cyclizes intermediate bto caprolactam include, but are not limited to, the TE domain from thevicenistatin PKS from Streptomyces halstedii (NCBI Accession No.BAD08360), the leinamycin PKS from Streptomyces atroolivaceus (NCBIAccession No. AF484556), the salinilactam PKS from Salinospora tropica(NCBI Accession No. YP_001159601), and the BE-14106 PKS fromStreptomyces sp. DSM 21069 (NCBI Accession No. FJ872523).

Load ACP and KS1 domains are on separate proteins in the native system.The PKS shown in FIG. 21 is synthesized so that this precise arrangementis maintained, hence the PKS is composed of two separate proteins thatinteract to produce caprolactam.

EXAMPLE 10 Production of the GABA Starter Unit

Butirosin is an aminoglycoside antibiotic that contains a2-hydroxy-4-aminobutyric (HABA) side chain attached to the N1 of thecentral sugar, 2-deoxystreptamine. The pathway for synthesis of HABA isshown in FIG. 22. The enzyme BtrJ is a biotin-dependentcarboxytransferase that transfers L-glutamic acid to BtrI, a stand-aloneacyl carrier protein (ACP) creating the thioester. This is acted upon bythe enzyme BtrK, a decarboxylase that produces 4-aminobutyryl-BtrI([gamma-amino butyratyl] GABA-ACP). The remainder of the pathway isshown in FIG. 22.

BtrI, BtrJ, and BtrK from Bacillus circulars (NCBI Accession Nos. BAE07073, BAE07074, and BAE07075, respectively), is synthesized de novoemploying the preferred codon usage for the host of choice. BtrI isaltered to create BtrI* to contain the docking domain to allow it tointeract with the KS domain of the PKS shown in FIG. 23. The KS-TEsegment of module 1 is identical to that described in FIG. 21. In theinstant scheme, a glutamyl-BtrI* thioester is formed through the actionof BtrJ. The glutamyl moiety is then decarboxylated by BtrK to producethe load ACP of the PKS acylated with the 4-aminobutyryl starter [a]. Asin the system shown in FIG. 21, this is converted to intermediate b andsubsequently released and cyclized to caprolactam.

EXAMPLE 11 Production of Caprolactam Using a PKS

A scheme for the biosynthesis of caprolactam is shown in FIG. 24. Theload module is composed of a segment containing the A domain and PCPdomain from module 7 of the oxazolomycin PKS. The A domain is specificfor loading glycine to the adjacent PCP domain. The KS domain of module1 is the KS domain of module 8 of the oxozolomycin PKS. The ACP-KS1segment of the PKS shown in FIG. 24 is taken from the oxozolomycin PKSfrom Streptomyces albus (NCBI Accession No. ABS90475. This segment isfused to a segment containing the remaining AT-DH-ER-KR-ACP domains ofmodule 2 and a full KS-AT-DH-ER-KR-ACP-TE-containing module 3. Theentire PKS is produced as a single ORF. The AT1-KS2 segment can be takenfrom a number of PKS modules that contain a malonyl-specific AT domainand the DH-ER-KR-ACP and adjacent downstream KS domain including, butnot limited to the AT-KS segment from AT5 through KS6 segment of thespirofungin PKS (Accession: Streptomyces violaceusniger Tü 4113 (wwwsite ncbi.nlm.nih.gov/nuccore/CP002994.1: Spirofungin cluster:Strvi_6572-Strvi_6584), or the AT5-ACP5 segment from the reveromycingene cluster Streptomyces sp. SN-593 (NCBI Accession No. AB568601), orthe AT6-KS6, or AT15-KS 16 segments of the nystatin PKS fromStreptomyces noursei (NCBI Accession No. AF263912). To avoid thepossibility of intra modular recombination, the AT-ACP segments ofmodules 2 and 3 are not from the same native modules. Preferred TEdomains shown in FIG. 24 that both releases and cyclizes intermediate bto caprolactam include, but are not limited to, the TE domain from thevicenistatin PKS from Streptomyces halstedii (NCBI Accession No.BAD08360), the leinamycin PKS from Streptomyces atroolivaceus (NCBIAccession No. AF484556), the salinilactam PKS from Salinospora tropica(NCBI Accession No. YP_001159601), and the BE-14106 PKS fromStreptomyces sp. DSM 21069 (NCBI Accession No. FJ872523).

EXAMPLE 12 Production of 6-Aminocaproic Acid Using a PKS

Three schemes for the biosynthesis pathway of 6-aminocaproic acid areshown in FIG. 25 A-C. Schemes A, B, C are use the identical PKS elementsand additional enzymes to produce intermediate a to the schems shown inFIGS. 22, 23, and 24, respectively, with the exception that the TEdomain for the production of caprolactam is replaced with a TE domainthat releases but does not cyclize intermediate b. Examples of such TEdomains include, but are not limited to TE domains from the niddamycinPKS from Streptomyces caelestis (NCBI Accession No. AF016585), theoligomycin PKS from Streptomyces avermitilis (NCBI Accession No.NC_003155), the epothilone PKS from Sorangium cellulosum (NCBI AccessionNo. AF217189), the pikromycin PKS from Streptomyces venezuelae (NCBIAccession No. BD232534.1), and the erythromycin PKS fromSaccharopolyspora erythraea (NCBI Accession No. M63677.1).

EXAMPLE 13 Production of 1,6-hexanediamine Using a PKS

Three schemes for the biosynthesis pathway of hexane-1,4-diamine areshown in FIG. 26 A-C. Schemes A, B, C are use the identical PKS elementsand additional enzymes to produce intermediate a to the schemes shown inFIGS. 22, 23, and 24, respectively, with the exception that the TEdomain for the production of caprolactam is replaced with the R domainfrom MxcG from Stigmatella aurantiaca (NCBI Accession No. AAG31130), andthe enzyme MxcL, an aldehyde aminotransferase from Stigmatellaaurantiaca (NCBI Accession No. AAG31130) is added to the host. The Rdomain and MxcL act to release the terminal intermediate b (FIGS. 26 A &B) or c (FIG. 26 C) from the PKS and aminate it to producehexane-1,4-diamine.

These approaches should yield the expected even-chain diacid. The PKSgenes described herein, or the hosts that carry them, are available fromthe American Type Culture Collection (ATCC) depository.

While the present invention has been described with reference to thespecific embodiments thereof, it should be understood by those skilledin the art that various changes may be made and equivalents may besubstituted without departing from the true spirit and scope of theinvention. In addition, many modifications may be made to adapt aparticular situation, material, composition of matter, process, processstep or steps, to the objective, spirit and scope of the presentinvention. All such modifications are intended to be within the scope ofthe claims appended hereto.

What is claimed is:
 1. A non-naturally occurring hybrid polyketidesynthase (PKS) which synthesizes adipic acid, wherein the PKS comprises:(a) a first module that is a loading module that incorporatessuccinyl-CoA, wherein the first module comprises an aspartate-specificadenylation (A) domain from the non-ribosomal peptide synthetase (NRPS)from the calcium-dependent antibiotic (CPA) pathway fromSaccharopolyspora erythraea linked to a peptidylcarrier protein (PCP)domain from the bleomycin pathway from Streptomyces verticillus; whereinthe A domain comprises a glutamine substitution for the conserved Asp235residue of the substrate-binding pocket as defined in the gramicidin Ssynthase phenylalanine-activating domain; and a second module comprisingat least one extension module and a TE domain; or (b) a first modulethat is a loading module that incorporates succinyl-CoA, wherein thefirst module comprises a loading domain and ACP domain of achondrochloren PKS in which a succinyl-CoA synthetase replaces a CoAligase domain and a second module comprising at least one extensionmodule and a TE domain; or (c) an etnangien loading module whichincorporates succinate using a trans-AT domain; and (i) at least oneheterologous extension module, and a TE domain: or (ii) extension module1 from Sorangium cellulosum PKS in which DH-ER-KR domains are insertedbetween the ACP2 and ACP3; and a TE domain; or (iii) wherein theetnangien loading module has inactivated the KS domain joined to the KSdomain of extension module 2 from Sorangium cellulosum PKS linked to amalonyl-specific AT domain joined to DH-ER-KR-ACP-TE domains; or (d) aloading module and at least three extension modules as set forth in FIG.14, wherein the PKS produces the intermediates [a], [b], [c], and [d]set forth in FIG. 14, wherein the 9-carbon backbone of [d] is releasedfrom the ACP by the TE domain and converted to adipic and propionic acidby an esterase, an alcohol dehydrogenase, a flavin-binding familymonooxygenase, and an aldehyde dehydrogenase as set forth in FIG.
 13. 2.The non-naturally occurring hybrid PKS of claim 1, wherein the PKScomprises the modules set forth in (a), wherein the at least oneextension module comprises a KS domain joined to an AT-DH-ER-KR-ACP fromnystatin module 5 or nystatin module 15 that incorporates malonyl-CoAand fully reduces a corresponding β-carbonyl group; and a TE domainfused to the ACP from the nystatin module 5 or
 15. 3. The non-naturallyoccurring hybrid PKS of claim 2, wherein the KS domain is from thebleomycin pathway from Streptomyces verticillus and the TE domain isfrom the erythromycin pathway.
 4. The PKS of claim 2, wherein the Adomain is directly linked to the PCP domain.
 5. The non-naturallyoccurring hybrid PKS of claim 1, wherein the PKS comprises the modulesset forth in (b) and wherein the at least one extension module comprisesa nystatin module 5; and a TE domain.
 6. The non-naturally occurringhybrid PKS of claim 1, wherein the PKS comprises the etnangien loadingmodule, the at least one heterologous extension module, and the TEdomain as set forth in (c) (i).
 7. The non-naturally occurring hybridPKS of claim 1, wherein the PKS comprises a loading module and threeextension modules as set forth in FIG. 14, wherein the PKS produces theintermediates [a], [b], [c], and [d] set forth in FIG. 14, wherein the9-carbon backbone of [d] is released from the ACP by the TE domain andconverted to adipic and propionic acid by an esterase, an alcoholdehydrogenase, a flavin-binding family monooxygenase, and an aldehydedehydrogenase as set forth in FIG.
 13. 8. The non-naturally occurringhybrid PKS of claim 1, wherein the PKS comprises the modules set forthin FIG. 11, and wherein the A domain is a variant of protein DhbE fromBacillus subtilis.
 9. A recombinant nucleic acid encoding thenon-naturally occurring hybrid polyketide synthase (PKS) of claim
 1. 10.A replicon comprising the recombinant nucleic acid of claim 9, whereinthe replicon is capable of stably maintained in a host cell.
 11. Thereplicon of claim 10, wherein the replicon is a plasmid or vector. 12.The replicon of claim 11, wherein the vector is an expression vector.13. A host cell comprising the recombinant nucleic acid of claim 9 orthe replicon of claim
 10. 14. The host cell of claim 13, wherein thehost cell when cultured produces adipic acid.
 15. A method of producingadipic acid comprising: culturing the host cell of claim 14 in asuitable culture medium such that adipic acid is produced.
 16. Themethod of claim 15, further comprising isolating the adipic acid. 17.The method of claim 16, further comprising reacting the adipic acid witha diamine to produce a nylon.